The mechanical properties of DNA play a critical role in many biological functions. For
example, DNA packing in viruses involves confining the viral genome in a volume (the viral …

The maintenance of intact genetic information, as well as the deployment of transcription for
specific sets of genes, critically rely on a family of proteins interacting with DNA and …

The wormlike chain model describes the micromechanics of semiflexible polymers by
introducing the persistence length. We propose a method of measuring the persistence …

Many DNA-modifying enzymes act in a manner that requires communication between two
noncontiguous DNA sites. These sites can be brought into contact either by a diffusion …

In many cases, transcriptional regulation involves the binding of transcription factors at sites
on the DNA that are not immediately adjacent to the promoter of interest. This action at a …

At many promoters, transcription is regulated by simultaneous binding of a protein to
multiple sites on DNA, but the structures and dynamics of such transcription factor-mediated …

Many biological processes involve enzymes moving along DNA. Such motion might be
impeded by DNA-bound proteins or DNA supercoils. Current techniques are incapable of …

The tethered particle motion (TPM) allows the direct detection of activity of a variety of
biomolecules at the single molecule level. First pioneered for RNA polymerase, it has …

To cleave DNA, Type III restriction enzymes must communicate the relative orientation of two
asymmetric recognition sites over hundreds of base pairs. The basis of this long-distance …

We show how to calculate the probability of DNA loop formation mediated by regulatory
proteins such as Lac repressor, using a mathematical model of DNA elasticity. Our approach …